The head of South Australia's Education Department, Keith Bartley, has resigned.

His decision to quit comes a fortnight after the release of the Debelle report, a royal commission which found significant failings within the department in its handling of an Adelaide western suburbs school sexual abuse case.

It made a raft of recommendations to clean up the system.

Premier Jay Weatherill said Mr Bartley had resigned for health and family reasons and would return to England.

He said Mr Bartley had acted because it became too difficult to balance personal matters with departmental needs.

"He's indicated to me that he doesn't believe he has the capacity to carry forward the work of the chief executive of the department for education," Mr Weatherill said.

"He's resigned because of his own health and because of concerns about his family and bringing his elderly parents. He has, for some time, been discussing these matters with me.

"We wanted him to make sure that he dealt with the initial response to the Debelle inquiry. He doesn't believe he's in a position to take forward the agenda in the future."

In a statement released later, Mr Bartley confirmed the decision to resign was his own and said he planned to retire when he and his wife returned to the UK, and would spend time with his first grandchild.

Mr Bartley was employed two years ago to mend relations between public schools and the central bureaucracy which had soured.

But it would be the Debelle inquiry - launched to investigate why parents at a school in Adelaide's west were not told about the arrest and later conviction of an after-school hours carer for the sexual assault of a student - which would be his biggest challenge.

By his own admission Mr Bartley said the inquiry showed a "sobering chronicle of failures" at every level in the department.

Mr Weatherill said there had been no government pressure on Mr Bartley to go.

"We've responded to the recommendations, we've taken some important first steps but he doesn't feel confident in being able to take the rest of the response forward nor leading such a large and important agency of this sort," Mr Weatherill said.

New leadership of the department welcomed

Former police assistant commissioner Tony Harrison has been appointed as Mr Bartley's replacement and the current head of schools, Garry Costello, will take on a new role of chief education officer.

The Government said Mr Harrison had strong experience on child protection as part of his policing career and established the sexual crimes investigation branch.

It said he was experienced in the disability sector and had worked with vulnerable children in his role as chairman at Minda.

"I've had a lot of partnership arrangements over many many years with people right across child protection, sexual crimes investigation," he said.

"But the reality is that in a department like this one there will be a wealth of talent.

"People who have provided support to parents, people who have acted as educators and facilitators and I'm sure together, as a large executive team, we will be able to work together to focus on some of the major priorities."

Parent Danyse Soester, the whistleblower at the centre of the Debelle inquiry, says Mr Bartley failed in his role and new blood is very much welcomed.